## [1] "data/config.vertebrata_minimal.yaml"
Analysis report - 22 January, 2023 - 19:51 CET - version: 0.9.7
Location of genomes files:
results/assemblies
Total number of included genomes: 0
Locally provided genomes: 0
Successfully downloaded genomes: 0
Failed species downloads: 0
Not downloaded:
Information on successfully downloaded genomes:
info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
if (file.size(downloaded_genomes_statistics_file) != 0) {
data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
} else {
info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
}
data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}
No information about downloaded genomes found. Did you run phylociraptor setup ?
Orthologous genes were inferred using BUSCO.
Location of BUSCO results:
results/orthology/busco
Used BUSCO set: vertebrata_odb10
Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
228730at7742, 164538at7742, 320238at7742
Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:
| species | single_copy | duplicated | fragmented | missing |
|---|---|---|---|---|
| Amblyraja_radiata | 2999 | 71 | 98 | 186 |
| Anolis_carolinensis | 2861 | 22 | 169 | 302 |
| Callorhinchus_milii | 2976 | 34 | 131 | 213 |
| Canis_lupus | 3122 | 47 | 65 | 120 |
| Danio_kyathit | 3107 | 45 | 75 | 127 |
| Dasypus_novemcinctus | 2717 | 61 | 212 | 364 |
| Eptatretus_burgeri | 1612 | 59 | 490 | 1193 |
| Gallus_gallus | 3180 | 29 | 45 | 100 |
| Homo_sapiens | 2984 | 130 | 77 | 163 |
| Latimeria_chalumnae | 2795 | 30 | 279 | 250 |
| Loxodonta_africana | 3039 | 22 | 103 | 190 |
| Meleagris_gallopavo | 2872 | 19 | 205 | 258 |
| Monodelphis_domestica | 3049 | 142 | 76 | 87 |
| Mus_musculus | 3124 | 55 | 51 | 124 |
| Neoceratodus_forsteri | 2101 | 75 | 723 | 455 |
| Notamacropus_eugenii | 1169 | 29 | 514 | 1642 |
| Oreochromis_niloticus | 3275 | 20 | 25 | 34 |
| Ornithorhynchus_anatinus | 3075 | 36 | 141 | 102 |
| Petromyzon_marinus | 2275 | 59 | 193 | 827 |
| Protopterus_annectens | 2029 | 1130 | 105 | 90 |
| Rana_temporaria | 3088 | 74 | 76 | 116 |
| Scyliorhinus_canicula | 2977 | 102 | 106 | 169 |
| Taeniopygia_guttata | 3161 | 19 | 50 | 124 |
| Takifugu_rubripes | 3120 | 77 | 73 | 84 |
| Xenopus_tropicalis | 3231 | 34 | 30 | 59 |
Location of alignment files:
results/alignments/full
| length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned.fas | 652 | 25 | 179 | 617 | 35 | 659 | 25 | 180 | 625 | 34 | 690 | 25 | 178 | 655 | 35 |
| 359032at7742_aligned.fas | 347 | 25 | 104 | 325 | 22 | 347 | 25 | 105 | 325 | 22 | 347 | 25 | 105 | 325 | 22 |
| 406935at7742_aligned.fas | 292 | 25 | 75 | 276 | 16 | 299 | 25 | 80 | 283 | 16 | 305 | 25 | 81 | 289 | 16 |
| 97645at7742_aligned.fas | 1237 | 24 | 290 | 1162 | 75 | 1320 | 24 | 287 | 1243 | 77 | 1399 | 24 | 291 | 1320 | 79 |
| 332227at7742_aligned.fas | 554 | 23 | 169 | 508 | 46 | 552 | 23 | 168 | 506 | 46 | 565 | 23 | 166 | 519 | 46 |
| 361842at7742_aligned.fas | 352 | 25 | 74 | 334 | 18 | 365 | 25 | 75 | 345 | 20 | 364 | 25 | 79 | 344 | 20 |
| 409625at7742_aligned.fas | 244 | 25 | 69 | 234 | 10 | 245 | 25 | 67 | 233 | 12 | 246 | 25 | 67 | 234 | 12 |
| 33940at7742_aligned.fas | 1351 | 25 | 102 | 1085 | 266 | 1394 | 25 | 111 | 1123 | 271 | 1397 | 25 | 103 | 1127 | 270 |
| 378120at7742_aligned.fas | 266 | 25 | 116 | 216 | 50 | 277 | 25 | 118 | 227 | 50 | 291 | 25 | 105 | 241 | 50 |
| 409719at7742_aligned.fas | 410 | 25 | 72 | 388 | 22 | 358 | 25 | 72 | 336 | 22 | 416 | 25 | 72 | 394 | 22 |
| 342641at7742_aligned.fas | 364 | 25 | 127 | 324 | 40 | 368 | 25 | 130 | 327 | 41 | 374 | 25 | 128 | 333 | 41 |
| 403632at7742_aligned.fas | 423 | 25 | 34 | 412 | 11 | 431 | 25 | 44 | 420 | 11 | 441 | 25 | 41 | 430 | 11 |
| 413149at7742_aligned.fas | 232 | 25 | 75 | 226 | 6 | 253 | 25 | 85 | 247 | 6 | 236 | 25 | 78 | 230 | 6 |
| 353318at7742_aligned.fas | 382 | 25 | 86 | 369 | 13 | 390 | 25 | 88 | 377 | 13 | 397 | 25 | 90 | 384 | 13 |
| 404316at7742_aligned.fas | 262 | 25 | 66 | 221 | 41 | 255 | 25 | 66 | 214 | 41 | 271 | 25 | 65 | 230 | 41 |
| 42971at7742_aligned.fas | 1327 | 23 | 448 | 1037 | 290 | 1351 | 23 | 462 | 1060 | 291 | 1372 | 23 | 464 | 1082 | 290 |
Location of trimmed alignment files:
results/alignments/trimmed
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 437 | 25 | 174 | 393 | 44 | 454 | 25 | 179 | 419 | 35 | 458 | 25 | 178 | 414 | 44 | 469 | 25 | 180 | 435 | 34 | 462 | 25 | 173 | 418 | 44 | 469 | 25 | 178 | 434 | 35 |
| 332227at7742_aligned_trimmed.fas | 292 | 23 | 144 | 227 | 65 | 298 | 23 | 169 | 252 | 46 | 293 | 23 | 143 | 228 | 65 | 299 | 23 | 168 | 253 | 46 | 292 | 23 | 143 | 227 | 65 | 296 | 23 | 166 | 250 | 46 |
| 33940at7742_aligned_trimmed.fas | 1113 | 25 | 101 | 800 | 313 | 1018 | 25 | 102 | 752 | 266 | 1129 | 25 | 110 | 808 | 321 | 1022 | 25 | 111 | 751 | 271 | 1107 | 25 | 102 | 788 | 319 | 1016 | 25 | 103 | 746 | 270 |
| 342641at7742_aligned_trimmed.fas | 274 | 25 | 118 | 232 | 42 | 259 | 25 | 127 | 219 | 40 | 288 | 25 | 127 | 246 | 42 | 264 | 25 | 130 | 223 | 41 | 291 | 25 | 121 | 249 | 42 | 265 | 25 | 128 | 224 | 41 |
| 353318at7742_aligned_trimmed.fas | 208 | 25 | 87 | 195 | 13 | 214 | 25 | 86 | 201 | 13 | 205 | 25 | 89 | 192 | 13 | 232 | 25 | 88 | 219 | 13 | 206 | 25 | 91 | 193 | 13 | 250 | 25 | 90 | 237 | 13 |
| 359032at7742_aligned_trimmed.fas | 165 | 25 | 103 | 141 | 24 | 254 | 25 | 104 | 232 | 22 | 165 | 25 | 103 | 141 | 24 | 170 | 25 | 105 | 148 | 22 | 164 | 25 | 102 | 140 | 24 | 191 | 25 | 105 | 169 | 22 |
| 361842at7742_aligned_trimmed.fas | 233 | 25 | 75 | 212 | 21 | 219 | 25 | 74 | 201 | 18 | 239 | 25 | 76 | 215 | 24 | 219 | 25 | 75 | 199 | 20 | 235 | 25 | 77 | 211 | 24 | 218 | 25 | 79 | 198 | 20 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 115 | 192 | 61 | 253 | 25 | 116 | 203 | 50 | 261 | 25 | 117 | 200 | 61 | 253 | 25 | 118 | 203 | 50 | 257 | 25 | 104 | 196 | 61 | 252 | 25 | 105 | 202 | 50 |
| 403632at7742_aligned_trimmed.fas | 177 | 25 | 32 | 162 | 15 | 166 | 25 | 34 | 155 | 11 | 190 | 25 | 41 | 175 | 15 | 171 | 25 | 44 | 160 | 11 | 189 | 25 | 41 | 174 | 15 | 171 | 25 | 41 | 160 | 11 |
| 404316at7742_aligned_trimmed.fas | 209 | 25 | 67 | 163 | 46 | 217 | 25 | 66 | 176 | 41 | 208 | 25 | 67 | 162 | 46 | 220 | 25 | 66 | 179 | 41 | 205 | 25 | 66 | 159 | 46 | 217 | 25 | 65 | 176 | 41 |
| 406935at7742_aligned_trimmed.fas | 139 | 25 | 75 | 119 | 20 | 204 | 25 | 75 | 188 | 16 | 146 | 25 | 80 | 124 | 22 | 207 | 25 | 80 | 191 | 16 | 147 | 25 | 81 | 125 | 22 | 206 | 25 | 81 | 190 | 16 |
| 409625at7742_aligned_trimmed.fas | 132 | 25 | 69 | 120 | 12 | 137 | 25 | 69 | 127 | 10 | 146 | 25 | 67 | 132 | 14 | 134 | 25 | 67 | 122 | 12 | 138 | 25 | 67 | 124 | 14 | 133 | 25 | 67 | 121 | 12 |
| 409719at7742_aligned_trimmed.fas | 130 | 25 | 72 | 107 | 23 | 227 | 25 | 72 | 205 | 22 | 134 | 25 | 72 | 111 | 23 | 151 | 25 | 72 | 129 | 22 | 130 | 25 | 72 | 107 | 23 | 229 | 25 | 72 | 207 | 22 |
| 413149at7742_aligned_trimmed.fas | 102 | 25 | 66 | 93 | 9 | 124 | 25 | 75 | 118 | 6 | 112 | 25 | 73 | 103 | 9 | 125 | 25 | 85 | 119 | 6 | 105 | 25 | 67 | 96 | 9 | 127 | 25 | 78 | 121 | 6 |
| 42971at7742_aligned_trimmed.fas | 929 | 23 | 410 | 619 | 310 | 1016 | 23 | 448 | 726 | 290 | 940 | 23 | 413 | 629 | 311 | 998 | 23 | 462 | 707 | 291 | 940 | 23 | 429 | 630 | 310 | 1026 | 23 | 464 | 736 | 290 |
| 97645at7742_aligned_trimmed.fas | 797 | 24 | 284 | 704 | 93 | 747 | 24 | 290 | 672 | 75 | 817 | 24 | 279 | 720 | 97 | 737 | 24 | 287 | 660 | 77 | 829 | 24 | 280 | 731 | 98 | 740 | 24 | 291 | 661 | 79 |
Location of filtered alignment files:
results/alignments/filtered
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 437 | 25 | 174 | 393 | 44 | 454 | 25 | 179 | 419 | 35 | 458 | 25 | 178 | 414 | 44 | 469 | 25 | 180 | 435 | 34 | 462 | 25 | 173 | 418 | 44 | 469 | 25 | 178 | 434 | 35 |
| 332227at7742_aligned_trimmed.fas | 292 | 23 | 144 | 227 | 65 | 298 | 23 | 169 | 252 | 46 | 293 | 23 | 143 | 228 | 65 | 299 | 23 | 168 | 253 | 46 | 292 | 23 | 143 | 227 | 65 | 296 | 23 | 166 | 250 | 46 |
| 33940at7742_aligned_trimmed.fas | 1113 | 25 | 101 | 800 | 313 | 1018 | 25 | 102 | 752 | 266 | 1129 | 25 | 110 | 808 | 321 | 1022 | 25 | 111 | 751 | 271 | 1107 | 25 | 102 | 788 | 319 | 1016 | 25 | 103 | 746 | 270 |
| 342641at7742_aligned_trimmed.fas | 274 | 25 | 118 | 232 | 42 | 259 | 25 | 127 | 219 | 40 | 288 | 25 | 127 | 246 | 42 | 264 | 25 | 130 | 223 | 41 | 291 | 25 | 121 | 249 | 42 | 265 | 25 | 128 | 224 | 41 |
| 353318at7742_aligned_trimmed.fas | 208 | 25 | 87 | 195 | 13 | 214 | 25 | 86 | 201 | 13 | 205 | 25 | 89 | 192 | 13 | 232 | 25 | 88 | 219 | 13 | 206 | 25 | 91 | 193 | 13 | 250 | 25 | 90 | 237 | 13 |
| 359032at7742_aligned_trimmed.fas | 165 | 25 | 103 | 141 | 24 | 254 | 25 | 104 | 232 | 22 | 165 | 25 | 103 | 141 | 24 | 170 | 25 | 105 | 148 | 22 | 164 | 25 | 102 | 140 | 24 | 191 | 25 | 105 | 169 | 22 |
| 361842at7742_aligned_trimmed.fas | 233 | 25 | 75 | 212 | 21 | 219 | 25 | 74 | 201 | 18 | 239 | 25 | 76 | 215 | 24 | 219 | 25 | 75 | 199 | 20 | 235 | 25 | 77 | 211 | 24 | 218 | 25 | 79 | 198 | 20 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 115 | 192 | 61 | 253 | 25 | 116 | 203 | 50 | 261 | 25 | 117 | 200 | 61 | 253 | 25 | 118 | 203 | 50 | 257 | 25 | 104 | 196 | 61 | 252 | 25 | 105 | 202 | 50 |
| 404316at7742_aligned_trimmed.fas | 209 | 25 | 67 | 163 | 46 | 217 | 25 | 66 | 176 | 41 | 208 | 25 | 67 | 162 | 46 | 220 | 25 | 66 | 179 | 41 | 205 | 25 | 66 | 159 | 46 | 217 | 25 | 65 | 176 | 41 |
| 406935at7742_aligned_trimmed.fas | 139 | 25 | 75 | 119 | 20 | 204 | 25 | 75 | 188 | 16 | 146 | 25 | 80 | 124 | 22 | 207 | 25 | 80 | 191 | 16 | 147 | 25 | 81 | 125 | 22 | 206 | 25 | 81 | 190 | 16 |
| 409625at7742_aligned_trimmed.fas | 132 | 25 | 69 | 120 | 12 | 137 | 25 | 69 | 127 | 10 | 146 | 25 | 67 | 132 | 14 | 134 | 25 | 67 | 122 | 12 | 138 | 25 | 67 | 124 | 14 | 133 | 25 | 67 | 121 | 12 |
| 409719at7742_aligned_trimmed.fas | 130 | 25 | 72 | 107 | 23 | 227 | 25 | 72 | 205 | 22 | 134 | 25 | 72 | 111 | 23 | 151 | 25 | 72 | 129 | 22 | 130 | 25 | 72 | 107 | 23 | 229 | 25 | 72 | 207 | 22 |
| 413149at7742_aligned_trimmed.fas | 102 | 25 | 66 | 93 | 9 | 124 | 25 | 75 | 118 | 6 | 112 | 25 | 73 | 103 | 9 | 125 | 25 | 85 | 119 | 6 | 105 | 25 | 67 | 96 | 9 | 127 | 25 | 78 | 121 | 6 |
| 42971at7742_aligned_trimmed.fas | 929 | 23 | 410 | 619 | 310 | 1016 | 23 | 448 | 726 | 290 | 940 | 23 | 413 | 629 | 311 | 998 | 23 | 462 | 707 | 291 | 940 | 23 | 429 | 630 | 310 | 1026 | 23 | 464 | 736 | 290 |
| 97645at7742_aligned_trimmed.fas | 797 | 24 | 284 | 704 | 93 | 747 | 24 | 290 | 672 | 75 | 817 | 24 | 279 | 720 | 97 | 737 | 24 | 287 | 660 | 77 | 829 | 24 | 280 | 731 | 98 | 740 | 24 | 291 | 661 | 79 |
Location of modeltesting files:
results/modeltest
Overview of individual modeltest results:
| alignment | clustalo-aliscore | clustalo-trimal | mafft-aliscore | mafft-trimal | muscle-aliscore | muscle-trimal |
|---|---|---|---|---|---|---|
| 193525at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 332227at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 33940at7742 | VT+R2 | VT+R2 | JTT+R2 | JTT+R2 | JTT+R2 | JTT+R2 |
| 342641at7742 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 |
| 353318at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 359032at7742 | LG+G4 | JTT+I+G4 | LG+G4 | JTT+G4 | LG+G4 | JTT+G4 |
| 361842at7742 | LG+G4 | JTTDCMut+G4 | LG+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 |
| 378120at7742 | LG+G4 | JTTDCMut+F+R3 | LG+G4 | JTTDCMut+F+R3 | LG+G4 | LG+G4 |
| 404316at7742 | JTT+R2 | JTT+R3 | JTT+R2 | JTT+R3 | JTT+R2 | JTT+R3 |
| 406935at7742 | LG+G4 | VT+G4 | LG+G4 | LG+G4 | LG+G4 | VT+G4 |
| 409625at7742 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 |
| 409719at7742 | LG+G4 | JTT+I+G4 | LG+G4 | JTTDCMut+G4 | LG+G4 | JTT+I+G4 |
| 413149at7742 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 |
| 42971at7742 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 |
| 97645at7742 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 |
Location of gene trees:
results/modeltest
| gene | clustalo-aliscore | clustalo-trimal | mafft-aliscore | mafft-trimal | muscle-aliscore | muscle-trimal |
|---|---|---|---|---|---|---|
| 193525at7742 | 86 | 87 | 84 | 88 | 85 | 87 |
| 332227at7742 | 84 | 87 | 83 | 85 | 83 | 85 |
| 33940at7742 | 85 | 83 | 84 | 84 | 80 | 80 |
| 342641at7742 | 78 | 76 | 78 | 77 | 80 | 77 |
| 353318at7742 | 81 | 82 | 81 | 81 | 80 | 84 |
| 359032at7742 | 78 | 79 | 78 | 76 | 79 | 80 |
| 361842at7742 | 81 | 79 | 77 | 78 | 77 | 78 |
| 378120at7742 | 79 | 73 | 77 | 73 | 77 | 77 |
| 404316at7742 | 80 | 81 | 82 | 84 | 76 | 79 |
| 406935at7742 | 68 | 74 | 68 | 79 | 72 | 78 |
| 409625at7742 | 77 | 74 | 80 | 85 | 79 | 82 |
| 409719at7742 | 65 | 78 | 69 | 71 | 67 | 71 |
| 413149at7742 | 76 | 78 | 77 | 79 | 75 | 79 |
| 42971at7742 | 86 | 86 | 85 | 86 | 87 | 88 |
| 97645at7742 | 85 | 85 | 83 | 83 | 83 | 84 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | boostraps | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|---|
| iqtree | clustalo | aliscore | 1000 | 0 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 50 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 60 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 70 | 13 | |
| iqtree | clustalo | aliscore | 1000 | 80 | 8 | |
| iqtree | clustalo | trimal | 1000 | 0 | 15 | |
| iqtree | clustalo | trimal | 1000 | 50 | 15 | |
| iqtree | clustalo | trimal | 1000 | 60 | 15 | |
| iqtree | clustalo | trimal | 1000 | 70 | 15 | |
| iqtree | clustalo | trimal | 1000 | 80 | 7 | |
| iqtree | mafft | aliscore | 1000 | 0 | 15 | |
| iqtree | mafft | aliscore | 1000 | 50 | 15 | |
| iqtree | mafft | aliscore | 1000 | 60 | 15 | |
| iqtree | mafft | aliscore | 1000 | 70 | 13 | |
| iqtree | mafft | aliscore | 1000 | 80 | 8 | |
| iqtree | mafft | trimal | 1000 | 0 | 15 | |
| iqtree | mafft | trimal | 1000 | 50 | 15 | |
| iqtree | mafft | trimal | 1000 | 60 | 15 | |
| iqtree | mafft | trimal | 1000 | 70 | 15 | |
| iqtree | mafft | trimal | 1000 | 80 | 8 | |
| iqtree | muscle | aliscore | 1000 | 0 | 15 | |
| iqtree | muscle | aliscore | 1000 | 50 | 15 | |
| iqtree | muscle | aliscore | 1000 | 60 | 15 | |
| iqtree | muscle | aliscore | 1000 | 70 | 14 | |
| iqtree | muscle | aliscore | 1000 | 80 | 7 | |
| iqtree | muscle | trimal | 1000 | 0 | 15 | |
| iqtree | muscle | trimal | 1000 | 50 | 15 | |
| iqtree | muscle | trimal | 1000 | 60 | 15 | |
| iqtree | muscle | trimal | 1000 | 70 | 15 | |
| iqtree | muscle | trimal | 1000 | 80 | 8 | |
| raxmlng | clustalo | aliscore | 100 | 0 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 50 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 60 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 70 | 13 | |
| raxmlng | clustalo | aliscore | 100 | 80 | 8 | |
| raxmlng | clustalo | trimal | 100 | 0 | 15 | |
| raxmlng | clustalo | trimal | 100 | 50 | 15 | |
| raxmlng | clustalo | trimal | 100 | 60 | 15 | |
| raxmlng | clustalo | trimal | 100 | 70 | 15 | |
| raxmlng | clustalo | trimal | 100 | 80 | 7 | |
| raxmlng | mafft | aliscore | 100 | 0 | 15 | |
| raxmlng | mafft | aliscore | 100 | 50 | 15 | |
| raxmlng | mafft | aliscore | 100 | 60 | 15 | |
| raxmlng | mafft | aliscore | 100 | 70 | 13 | |
| raxmlng | mafft | aliscore | 100 | 80 | 8 | |
| raxmlng | mafft | trimal | 100 | 0 | 15 | |
| raxmlng | mafft | trimal | 100 | 50 | 15 | |
| raxmlng | mafft | trimal | 100 | 60 | 15 | |
| raxmlng | mafft | trimal | 100 | 70 | 15 | |
| raxmlng | mafft | trimal | 100 | 80 | 8 | |
| raxmlng | muscle | aliscore | 100 | 0 | 15 | |
| raxmlng | muscle | aliscore | 100 | 50 | 15 | |
| raxmlng | muscle | aliscore | 100 | 60 | 15 | |
| raxmlng | muscle | aliscore | 100 | 70 | 14 | |
| raxmlng | muscle | aliscore | 100 | 80 | 7 | |
| raxmlng | muscle | trimal | 100 | 0 | 15 | |
| raxmlng | muscle | trimal | 100 | 50 | 15 | |
| raxmlng | muscle | trimal | 100 | 60 | 15 | |
| raxmlng | muscle | trimal | 100 | 70 | 15 | |
| raxmlng | muscle | trimal | 100 | 80 | 8 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|
| astral | clustalo | aliscore | 0 | 15 | |
| astral | clustalo | aliscore | 50 | 15 | |
| astral | clustalo | aliscore | 60 | 15 | |
| astral | clustalo | aliscore | 70 | 13 | |
| astral | clustalo | aliscore | 80 | 8 | |
| astral | clustalo | trimal | 0 | 15 | |
| astral | clustalo | trimal | 50 | 15 | |
| astral | clustalo | trimal | 60 | 15 | |
| astral | clustalo | trimal | 70 | 15 | |
| astral | clustalo | trimal | 80 | 7 | |
| astral | mafft | aliscore | 0 | 15 | |
| astral | mafft | aliscore | 50 | 15 | |
| astral | mafft | aliscore | 60 | 15 | |
| astral | mafft | aliscore | 70 | 13 | |
| astral | mafft | aliscore | 80 | 8 | |
| astral | mafft | trimal | 0 | 15 | |
| astral | mafft | trimal | 50 | 15 | |
| astral | mafft | trimal | 60 | 15 | |
| astral | mafft | trimal | 70 | 15 | |
| astral | mafft | trimal | 80 | 8 | |
| astral | muscle | aliscore | 0 | 15 | |
| astral | muscle | aliscore | 50 | 15 | |
| astral | muscle | aliscore | 60 | 15 | |
| astral | muscle | aliscore | 70 | 14 | |
| astral | muscle | aliscore | 80 | 7 | |
| astral | muscle | trimal | 0 | 15 | |
| astral | muscle | trimal | 50 | 15 | |
| astral | muscle | trimal | 60 | 15 | |
| astral | muscle | trimal | 70 | 15 | |
| astral | muscle | trimal | 80 | 8 |
## Thu Jul 7 15:40:41 CEST 2022 - Pipeline part 1 (orthology) done.
## Thu Jul 7 15:41:32 CEST 2022 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Thu Jul 7 15:41:34 CEST 2022 - Number of BUSCO sequence files: 16
## Thu Jul 7 15:41:34 CEST 2022 - Number of deduplicated BUSCO sequence files: 16
## Thu Jul 7 15:41:34 CEST 2022 - Pipeline part filter-orthology done.
## Sat Jan 21 17:38:39 CET 2023 - Pipeline part 2 (align) done.
## Sat Jan 21 17:40:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:13 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:13 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:18 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:18 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:22 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:22 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:23 CET 2023 - Number of alignments (mafft): 16
## Sat Jan 21 17:40:23 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Sat Jan 21 17:40:23 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (clustalo): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (muscle): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (mafft): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (muscle): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (clustalo): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Sat Jan 21 17:40:43 CET 2023 - Pipeline part filter_align done.
## Sat Jan 21 17:50:17 CET 2023 - Pipeline part modeltest (model) done.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:22 CET 2023 - Speciestree reconstruction done.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:17 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:17 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:18 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 18:08:20 CET 2023 - Pipeline part 3 (tree) done.
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:55 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:56 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:56 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 19:46:44 CET 2023 - Pipeline part 3 (tree) done.